[PyMOL] python module in pymol
Hi, I tried to use the "cluster_count" script (http://www.pymolwiki.org/index.php/Cluster_Count) in a pymol.pml file. Unfortunately I get the following message: --- PyMOL>cluster_count PO4 Traceback (most recent call last): File "/home/sws2/Desktop/pymol/modules/pymol/parser.py", line 464, in parse exec(layer.com2+"\n",self.pymol_names,self.pymol_names) File "", line 1 cluster_count PO4 ^ SyntaxError: invalid syntax --- (PO4) is a selection of five atoms When I use the same script as a pymol plugin, it works fine when I type in the command "cluster_count PO4" Any idea ??? Thanks for helping, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr - -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] python module in pymol
Hi Pascal, PyMOL treats .pml and .py files differently. The "cluster_count" script was written as a .py file as needs to be used as such. run cluster_count.py cluster_count PO4 worked just fine when run as a Python file. Cheers, -- Jason On Tue, Jul 9, 2013 at 6:06 AM, Pascal Auffinger wrote: > Hi, > > I tried to use the "cluster_count" script > (http://www.pymolwiki.org/index.php/Cluster_Count) > in a pymol.pml file. Unfortunately I get the following message: > --- > PyMOL>cluster_count PO4 > Traceback (most recent call last): > File "/home/sws2/Desktop/pymol/modules/pymol/parser.py", line 464, in > parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1 > cluster_count PO4 >^ > SyntaxError: invalid syntax > --- > (PO4) is a selection of five atoms > > When I use the same script as a pymol plugin, it works fine > when I type in the command "cluster_count PO4" > > Any idea ??? > > Thanks for helping, > > Pascal > > > > - > Pascal Auffinger > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex > > p.auffin...@ibmc-cnrs.unistra.fr > - > > > -- > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] python module in pymol
Dear Pascal, Do you have any errors/warning when launching PyMOL? If you fetch a structure in your PML file, be sure that the structure is downloaded before to start the plugin (use: fetch pdb_code, async=0) Can you send me some part of your PML file, so I can help you to debug? Best regards, Jerome Pansanel Le mardi 09 juillet 2013 à 13:06 +0200, Pascal Auffinger a écrit : > Hi, > > > I tried to use the "cluster_count" script > (http://www.pymolwiki.org/index.php/Cluster_Count) > in a pymol.pml file. Unfortunately I get the following message: > --- > PyMOL>cluster_count PO4 > Traceback (most recent call last): > File "/home/sws2/Desktop/pymol/modules/pymol/parser.py", line 464, > in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1 > cluster_count PO4 >^ > SyntaxError: invalid syntax > --- > (PO4) is a selection of five atoms > > > When I use the same script as a pymol plugin, it works fine > when I type in the command "cluster_count PO4" > > > Any idea ??? > > > Thanks for helping, > > > Pascal > > > > > > - > Pascal Auffinger > IBMC/CNRS > 15 rue René Descartes > 67084 Strasbourg Cedex > > > p.auffin...@ibmc-cnrs.unistra.fr > - > > > -- > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > ___ PyMOL-users mailing list > (PyMOL-users@lists.sourceforge.net) Info Page: > https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol movie
Hi Appu, interpolation between two conformations is called "morphing". You can do this with the incentive version of PyMOL, which includes an additional component called RigiMOL. With incentive PyMOL 1.6, you can morph directly from the object menu: A > generate > morph See also: http://pymolwiki.org/index.php/Morph (PyMOL 1.6) http://pymolwiki.org/index.php/Rigimol.morph (older PyMOL versions) Hope that helps. Cheers, Thomas Appu kumar wrote, On 07/09/13 07:13: > Dear All, > I am working on an enzyme which close it active site > when react with substrate. I have solved the structure in both open and > closed conformation. Now i want to make the movie of showing a series of > change in going from open to close conformation. please tell me how to > mkae movie. > Thank you > Appu -- Thomas Holder PyMOL Developer Schrödinger Contractor -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
